A central integrator of transcription networks in plant stress and energy signalling

The SnRK1 kinase TaSnRK1.10 positively regulates heavy metal chromium tolerance mainly by mediating reactive oxygen species homeostasis and activating the phenylpropanoid biosynthetic pathway in wheat

The sucrose non-fermenting-1 (SNF1)-related kinase (SnRK1) family plays key roles in multiple plant processes. However, limited information about its role in chromium (Cr) tolerance is available. Here, we identified an SnRK1 member (TaSnRK1.10) and functionally characterised its role in Cr tolerance in wheat. Cas9-TaSnRK1.10 lines exhibited decreased Cr tolerance and accumulated more Cr than the wheat variety ZM7698 under Cr stress conditions. TaSnRK1.10-overexpression lines displayed opposite phenotypes. Root phenotypic analysis showed that TaSnRK1.10 altered the root morphology by affecting total root length, average root diameter, and root surface area, especially under Cr stress conditions. Further physiological analysis showed that the regulation of Cr tolerance mediated by TaSnRK1.10 was related to reactive oxygen species (ROS) homeostasis. Additionally, transcriptomic analysis suggested that the significantly differentially expressed genes in the Cr stress group were mainly enriched in the phenylpropanoid biosynthetic pathway, which was confirmed by quantitative polymerase chain reaction analysis, implying that the phenylpropanoid pathway plays a key role in the regulation of Cr tolerance mediated by TaSnRK1.10. Collectively, our research revealed that TaSnRK1.10 positively regulates Cr tolerance, mainly by mediating ROS homeostasis and activating the phenylpropanoid biosynthetic pathway, thus providing a candidate target for the genetic manipulation of Cr resistance in wheat.

Sucrose transporter systems in cotyledons (or pre-existing leaves), as integrators of multiple signals, regulate stomatal development of all leaves

The dynamic optimization of photosynthetic production, which includes the synthesis of sucrose and glucose, is crucial for maintaining the balance between source and sink organs. This balance, in turn, determines plant growth, development, acclimation, and stress responses. The optimization of photosynthetic efficiency largely depends on the efficient transport of sugars produced through photosynthesis from the leaves. Stomata are pores found in the epidermis of stems or leaves that modulate both plant gas exchange and water/nutrient uptake. It has been investigated that the molecular mechanisms by which the stomatal development of systemic leaves is synergistically controlled by sucrose transporter systems enhance plant acclimation and stress tolerance. In this review, we summarize the current knowledge concerning the regulation of sugar signaling-mediated stomatal development and sucrose transport, focusing on the model species Arabidopsis thaliana and crop plants. This review provides novel insights into how sucrose transporter systems within cotyledons (or pre-existing leaves), as integrators of multiple signals, control the stomatal development of all leaves (including cotyledons or pre-existing leaves) under diverse exogenous and endogenous signals, to elevate plant acclimation and stress responses. This is achieved by integrating both exogenous and endogenous signals to modulate the process.

TaWUS-like-5D affects grain weight and filling by inhibiting the expression of sucrose and trehalose metabolism-related genes in wheat grain endosperm

Plant-specific WUSCHEL-related homeobox (Wox) transcription factors (TFs) are crucial for plant growth and development. However, the molecular mechanism of Wox-mediated regulation of thousand kernel weight (TKW) in crops remains elusive. In this research, we identified a major TKW-associated quantitative trait locus (QTL) on wheat chromosome 5DS by performing a genome-wide association study (GWAS) of a Chinese wheat mini-core collection (MCC) in four environments combined by bulked segregant analysis (BSA) and bulked segregant RNA-sequencing (BSR-seq) of wheat grains exhibiting a wide range of TKWs. The candidate TaWUS-like-5D was highly expressed in developing grains and was found to strongly negative influence grain TKW and wheat yield. Meanwhile, the RNAi lines, CRISPR/Cas9-edited single and double knockout mutants (AABBdd and AAbbdd), as well as the stop-gained aaBB Kronos mutants, exhibited a significant increase in grain size and TKW (P < 0.05 or P < 0.01) and a 10.0% increase in yield (P < 0.01). Further analyses indicated that TaWUS-like-5D regulates TKW by inhibiting the transcription of sucrose, hormone and trehalose metabolism-related genes, subsequently sharply decreasing starch synthesis in wheat grains. The results of this study provide a fundamental molecular basis for further elucidating the mechanism of Wox-mediated regulation of grain development in crops.

The Pseudoenzyme β-Amylase9 From Arabidopsis Activates α-Amylase3: A Possible Mechanism to Promote Stress-Induced Starch Degradation

Starch accumulation in plants provides carbon for nighttime use, for regrowth after periods of dormancy, and for times of stress. Both ɑ- and β-amylases (AMYs and BAMs, respectively) catalyze starch hydrolysis, but their functional roles are unclear. Moreover, the presence of catalytically inactive amylases that show starch excess phenotypes when deleted presents questions on how starch degradation is regulated. Plants lacking one of these catalytically inactive β-amylases, BAM9, have enhanced starch accumulation when combined with mutations in BAM1 and BAM3, the primary starch degrading BAMs in response to stress and at night, respectively. BAM9 has been reported to be transcriptionally induced by stress although the mechanism for BAM9 function is unclear. From yeast two-hybrid experiments, we identified the plastid-localized AMY3 as a potential interaction partner for BAM9. We found that BAM9 interacted with AMY3 in vitro and that BAM9 enhances AMY3 activity about three-fold. Modeling of the AMY3-BAM9 complex predicted a previously undescribed alpha-alpha hairpin in AMY3 that could serve as a potential interaction site. Additionally, AMY3 lacking the alpha-alpha hairpin is unaffected by BAM9. Structural analysis of AMY3 showed that it can form a homodimer in solution and that BAM9 appears to replace one of the AMY3 monomers to form a heterodimer. The presence of both BAM9 and AMY3 in many vascular plant lineages, along with model-based evidence that they heterodimerize, suggests that the interaction is conserved. Collectively these data suggest that BAM9 is a pseudoamylase that activates AMY3 in response to cellular stress, possibly facilitating stress recovery.

The oxidative stress 3-like protein GsOS3L, substrate of GsSnRK1, enhances salt and cadmium stresses in soybean roots

Salt and heavy metal stresses have significant impacts on crop growth and agricultural development. Wild soybean (Glycine soja) exhibits greater resistance to abiotic stresses than its cultivated counterpart (Glycine max). In this study, the oxidative stress 3-like gene GsOS3L was identified from yeast two hybridization cDNA library constructed from wild soybean RNA. 150 mM NaCl and 10 % PEG induced their expression in roots, stems and leaves, respectively. pGsOS3L:GUS activity was enhanced in various tissues with increasing NaCl and CdCl2 concentrations. Y2H, BiFC, and LCI activity assays revealed that GsOS3L interacted physically with the GsSnRK1 kinase. The GsOS3L protein, which contains potential phosphorylation and palmitoylation sites, was localized to the nucleus under normal conditions but translocated from the nucleus to the cell membrane under cadmium stress. This translocation was prevented by the palmitoylation inhibitor 2-bromopalmitate (2-BP) and by double mutation of the predicted palmitoylation sites (C4S/C21S). 2-BP treatment attenuated GsOS3L transgenic composite soybeans' cadmium stress tolerance. GsOS3L was found to be phosphorylated by GsSnRK1, which reduced the salt and cadmium stress tolerance of transgenic Arabidopsis plants. The findings of this study provide promising insights into the physiological and molecular mechanisms of GsOS3L in soybean under salt and cadmium stresses.

Identification of miRNA-mRNA regulatory network during the germination of soybean seed (Glycine max) and the role of Gma-miR1512a-GmKIN10 interaction

Seed germination is a key and complex physiological process in plant life, including soybeans. Here, we explored the miRNA-mRNA transcriptome changes and the key genes in the germination stages of the soybean. Morphological analysis showed that the imbibition of seeds was completed at 12 h, and the embryo broke through the seed coat at 36 h. During seed germination, mRNA and miRNA sequencing identified 20845 differentially expressed mRNAs (DEMs) and 421 differentially expressed miRNAs (DEMIs) at three specific time points: 12 h, 36 h, and 108 h. KEGG enrichment revealed that plant hormone signal transduction, plant-pathogen interaction and MAPK signaling pathway-plant were the crucial biological processes for seed germination. ABA and GA related DEMs on plant hormone signal transduction were abundant. miRNA-mRNA integrated analysis showed that 5170 miRNA-mRNA pairs were found. During germination, 20 significant miRNA-mRNA interactions were identified, involving the top 10 differentially expressed miRNAs (DEMIs) and 198 differentially expressed mRNAs (DEMs). Interestingly, the expression level of Gma-miR1512a increased significantly during soybean seed germination. This miRNA specifically regulates GmKIN10, homologous to AtKIN10, which mediates germination. To verify this interaction, co-agroinjection of GmKIN10-GFP/GUS and Gma-miR1512a into tobacco leaves demonstrated that Gma-miR1512a can inhibit GmKIN10 expression by cleaving its target site. Furthermore, the function of Gma-miR1512a-GmKIN10 were verified by overexpression transgene. Although Arabidopsis seeds overexpressing Gma-miR1512a (OE-Gma-miR1512a) showed no significant differences in germination indices compared to wild-type (WT) seeds, those overexpressing GmKIN10 (OE-GmKIN10) exhibited significantly lower germination indices. The seeds germination index of GmKIN10 and Gma-miR1512a double overexpression lines recovered. Additionally, the yeast two-hybrid assay, protein interaction prediction,and molecular docking all showed that GmKIN10 might interact with GmPP2A and GmDSP4. This study identified a complex miRNA-mRNA regulatory network that plays a crucial role in soybean seed germination. Specifically, Gma-miR1512a was found to regulate GmKIN10, significantly influencing germination rates and hormone signaling pathways.

Trehalose-6-Phosphate Phosphatase SlTPP1 Adjusts Diurnal Carbohydrate Partitioning in Tomato

Trehalose 6-phosphate phosphatases (TPPs) play essential roles in carbohydrate distribution between source and sink organs in plants. Here, we show that TPPs also participate in regulating diurnal carbohydrate partitioning. In tomato, SlTPP1 exhibited high expression in leaves, particularly in phloem, with distinct diurnal variation. Overexpression of SlTPP1 promoted plant growth and biomass accumulation, whereas its knockout reduced both. Analysis of photosynthesis parameters revealed that overexpression of SlTPP1 accelerated the initiation of photosynthesis at dawn, promoting assimilate production. Additionally, SlTPP1 enhanced the stem's buffering capacity in diurnal carbohydrate partitioning, promoting daytime carbohydrate accumulation and facilitating nocturnal carbohydrate export to the roots, resulting in increased root carbohydrate levels. These results indicate that SlTPP1 regulates diurnal carbohydrate partitioning, establishing a positive feedback loop that promotes plant growth. Notably, overexpression of SlTPP1 reduced T6P concentration, whereas overexpression of SnRK1 (sucrose non-fermenting 1-related protein kinase) α subunit (SNF1) decreased biomass and did not enhance the stem's buffering capacity in carbohydrate partitioning. These findings suggest that SlTPP1's regulation of diurnal carbohydrate partitioning is at least partially independent of the classical T6P-SnRK1 pathway.

Target of Rapamycin (TOR): A Master Regulator in Plant Growth, Development, and Stress Responses

The target of rapamycin (TOR) is a central regulator of growth, development, and stress adaptation in plants. This review delves into the molecular intricacies of TOR signaling, highlighting its conservation and specificity across eukaryotic lineages. We explore the molecular architecture of TOR complexes, their regulation by a myriad of upstream signals, and their consequential impacts on plant physiology. The roles of TOR in orchestrating nutrient sensing, hormonal cues, and environmental signals are highlighted, illustrating its pivotal function in modulating plant growth and development. Furthermore, we examine the impact of TOR on plant responses to various biotic and abiotic stresses, underscoring its potential as a target for agricultural improvements. This synthesis of current knowledge on plant TOR signaling sheds light on the complex interplay between growth promotion and stress adaptation, offering a foundation for future research and applications in plant biology.

Stable and dynamic gene expression patterns over diurnal and developmental timescales in Arabidopsis thaliana

Developmental processes are known to be circadian-regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals that entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diel oscillations of the Arabidopsis transcriptome have typically been measured in seedlings. We collected RNA sequencing (RNA-seq) data from Arabidopsis leaves over developmental and diel timescales, concurrently: every 4 h d-1, on three separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diel timescale, including genes related to a key energy sensor: the sucrose nonfermenting-1-related protein kinase complex. Moreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diel patterns that varied in amplitude, but not phase, over development. Some previously identified reverse transcription quantitative polymerase chain reaction housekeeping genes display undesirable levels of variation over both timescales. We identify which common reverse transcription quantitative polymerase chain reaction housekeeping genes are most stable across developmental and diel timescales. In summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diel patterns of expression change over developmental timescales.

Pupylation-Based Proximity Labeling Unravels a Comprehensive Protein and Phosphoprotein Interactome of the Arabidopsis TOR Complex

Target of rapamycin (TOR) is a signaling hub that integrates developmental, hormonal, and environmental signals to optimize carbon allocation and plant growth. In plant cells, TOR acts together with the proteins LST8-1 and RAPTOR1 to form a core TOR complex (TORC). While these proteins comprise a functional TORC, they engage with many other proteins to ensure precise signal outputs. Although TORC interactions have attracted significant attention in the recent past, large parts of the interactome are still unknown. In this resource study, PUP-IT is adapted, a fully endogenously expressed protein proximity labeling toolbox, to map TORC protein-protein interactions using the core set of TORC as baits. It is outlined how this interactome is differentially phosphorylated during changes in carbon availability, uncovering putative direct TOR kinase targets. An AlphaFold-Multimer approach is further used to validate many interactors, thus outlining a comprehensive TORC interactome that includes over a hundred new candidate interactors and provides an invaluable resource to the plant cell signaling community.

Hormesis effect of cadmium on pakchoi growth: Unraveling the ROS-mediated IAA-sugar metabolism from multi-omics perspective

Previous research on cadmium (Cd) focused on toxicity, neglecting hormesis and its mechanisms. In this study, pakchoi seedlings exposed to varying soil Cd concentrations (CK, 5, 10, 20, 40 mg/kg) showed an inverted U-shaped growth trend (hormesis characteristics): As Cd concentration increases, biomass exhibited hormesis character (Cd5) and then disappear (Cd40). ROS levels rose in both Cd treatments, with Cd5 being intermediate between CK and Cd40. But Cd5 preserved cellular structure, unlike damaged Cd40, hinting ROS in Cd5 acted as signaling regulators. To clarify ROS controlled subsequent metabolic processes, a multi-omics study was conducted. The results revealed 143 DEGs and 793 DEMs across all Cd treatment. KEGG indicated among all Cd treatments, the functional differences encompass: "plant hormone signal transduction" and "starch and sucrose metabolism". Through further analysis, we found that under the influence of ROS, the expression of IAA synthesis and signaling-related genes was significantly up-regulated, especially under Cd5 treatment. This further facilitated the accumulation of reducing sugars, which provided more energy for plant growth. Our research results demonstrated the signaling pathway involving ROS-IAA-Sugar metabolism, thereby providing a novel theoretical basis for cultivating more heavy metal hyperaccumulator crops and achieving phytoremediation of contaminated soils.

Genome-Wide Investigation of CPK-Related Kinase (CRK) Gene Family in Arabidopsis thaliana

Calcium-dependent protein kinase (CPK), representing a group of typical Ca2+ sensors in plants, has been well characterized in plants. CPK is capable of binding to Ca2+, which sequentially activates CPK. CPK-related kinase (CRK) shows protein structures similar to CPK but only contains degenerative EF-hands, which likely makes the activation of CRK Ca2+ independent. Compared with CPK, CRK is barely functionally analyzed. In this study, we systematically investigated CRK genes in the Arabidopsis genome. We found that CRK appeared to emerge in land plants, suggesting CPK and CRK are divided at very early stages during plant evolution. In Arabidopsis, the detailed analysis of the calmodulin-like domain of CRK indicated the substitutions of key amino acid residues in its EF-hands result in disrupted Ca2+ association. Next, by using a YFP tag, we found that all Arabidopsis CRK proteins were localized at the plasma membrane. After cloning the promoters of all eight CRK genes, we found that CRKs were widely expressed at all stages of Arabidopsis by using GUS staining. Furthermore, the kinase activity of CRK was examined by using phospho-antibody and Pro-Q staining. CRK was shown to possess high autophosphorylation, which was not affected by the presence of Ca2+. Moreover, we analyzed the cis-elements of CRK promoters and discovered that stress signals potentially regulate the expression of CRK genes. Consistently, by using quantitative real-time PCR (qPCR), we found a number of CRK genes were regulated by a variety of biotic and abiotic treatments such as flg22, ABA, drought, salt, and high and low temperatures. Furthermore, by utilizing proteomic approaches, we identified more than 100 proteins that interacted with CRK5 in planta. Notably, RLK and channels/transporters were found in CRK5-containing complexes, suggesting they function upstream and downstream of CRK, respectively.

The SnRK1-JMJ15-CRF6 module integrates energy and mitochondrial signaling to balance growth and the oxidative stress response in Arabidopsis

Mitochondria support plant growth and adaptation via energy production and signaling pathways. However, how mitochondria control the transition between growth and stress response is largely unknown in plants. Using molecular approaches, we identified the histone H3K4me3 demethylase JMJ15 and the transcription factor CRF6 as targets of SnRK1 in Arabidopsis. By analyzing antimycin A (AA)-triggered mitochondrial stress, we explored how SnRK1, JMJ15, and CRF6 form a regulatory module that gauges mitochondrial status to balance growth and the oxidative stress response. SnRK1a1, a catalytic α-subunit of SnRK1, phosphorylates and destabilizes JMJ15 to inhibit its H3K4me3 demethylase activity. While SnRK1a1 does not phosphorylate CRF6, it promotes its degradation via the proteasome pathway. CRF6 interacts with JMJ15 and prevents its SnRK1a1 phosphorylation-dependent degradation, forming an antagonistic feedback loop. SnRK1a1, JMJ15, and CRF6 are required for transcriptional reprogramming in response to AA stress. The transcriptome profiles of jmj15 and crf6 mutants were highly correlated with those of plants overexpressing SnRK1a1 under both normal and AA stress conditions. Genetic analysis revealed that CRF6 acts downstream of SnRK1 and JMJ15. Our findings identify the SnRK1-JMJ15-CRF6 module that integrates energy and mitochondrial signaling for the growth-defense trade-off, highlighting an epigenetic mechanism underlying mitonuclear communication.

Sugar sensors in plants: Orchestrators of growth, stress tolerance, and hormonal crosstalk

Sugars, vital metabolites for cellular health, play a central role in regulating diverse intracellular pathways that control plant growth and development. They also enhance stress responses, enabling plants to endure adverse conditions. A few intracellular molecules involved in sensing the intracellular sugar content and concomitantly facilitating appropriate response (growth or survivability) are known as sugar sensors. Among the numerous sugar sensors identified in plants, this review focuses on four extensively studied sugar sensors, namely hexokinase (HXK), Sucrose non-fermenting 1-related kinase-1 (Snf1-related kinase-1 or SnRK1), Target of rapamycin (TOR), and trehalose 6-phosphate (T6P). This review explores the multifaceted functions of these sugar sensors, highlighting their critical role in balancing energy metabolism and coordinating physiological processes under optimal and adverse conditions. By analyzing their involvement in plant growth, development, and stress response, this review underscores the significance of these sensors throughout the plant life cycle. Furthermore, this review highlights the intricate interplay among these sugar sensors, demonstrating how their activities are finely tuned and interdependent. We also examined the crosstalk between these sugar sensors and phytohormones, fine-tuning plant responses to environmental stimuli. Altogether, this review elucidates the significance of sugar sensors as integrators of metabolic and hormonal signals, providing a comprehensive understanding of their pivotal roles in plant biology. This knowledge paves the way for potential agricultural innovations to enhance crop productivity and resilience in the face of climate change.

Phenotype Assessment and Putative Mechanisms of Ammonium Toxicity to Plants

Ammonium (NH4+) and nitrate (NO3-) are the primary inorganic nitrogen (N) sources that exert influence on plant growth and development. Nevertheless, when NH4+ constitutes the sole or dominant N source, it can inhibit plant growth, a process also known as ammonium toxicity. Over multiple decades, researchers have shown increasing interest in the primary causes, mechanisms, and detoxification strategies of ammonium toxicity. Despite this progress, the current investigations into the mechanisms of ammonium toxicity remain equivocal. This review initially presents a comprehensive assessment of phenotypes induced by ammonium toxicity. Additionally, this review also recapitulates the existing mechanisms of ammonium toxicity, such as ion imbalance, disruption of the phytohormones homeostasis, ROS (reactive oxygen species) burst, energy expenditure, and rhizosphere acidification. We conclude that alterations in carbon-nitrogen (C-N) metabolism induced by high NH4+ may be one of the main reasons for ammonium toxicity and that SnRK1 (Sucrose non-fermenting 1-related kinase) might be involved in this process. The insights proffered in this review will facilitate the exploration of NH4+ tolerance mechanisms and the development of NH4+-tolerant crops in agricultural industries.

Signalling and regulation of plant development by carbon/nitrogen balance

The two most abundant macronutrients in plant cells are carbon (C) and nitrogen (N). Coordination of their cellular metabolism is a fundamental factor in guaranteeing the optimal growth and development of plants. N availability and assimilation profoundly affect plant gene expression and modulate root and stem architecture, thus affecting whole plant growth and crop yield. N status also affects C fixation, as it is an important component of the photosynthetic machinery in leaves. Reciprocally, increasing C supply promotes N uptake and assimilation. There is extensive knowledge of the different mechanisms that plants use for sensing and signalling their nutritional status to regulate the assimilation, metabolism and transport of C and N. However, the crosstalk between C and N pathways has received much less attention. Plant growth and development are greatly affected by suboptimal C/N balance, which can arise from nutrient deficiencies or/and environmental cues. Mechanisms that integrate and respond to changes in this specific nutritional balance have started to arise. This review will examine the specific responses to C/N imbalance in plants by focusing on the main inorganic and organic metabolites involved, how they are sensed and transported, and the interconnection between the early signalling components and hormonal networks that underlies plants' adaptive responses.

The E3 ubiquitin ligase TaGW2 facilitates TaSnRK1γ and TaVPS24 degradation to enhance stripe rust susceptibility in wheat

Wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), threatens global wheat production, and therefore discovering genes involved in stripe rust susceptibility is essential for balancing yield with disease resistance in sustainable breeding strategies. Although TaGW2 is well known to negatively regulate wheat kernel size and weight, its role in stress response remains unclear. Here, we found that TaGW2 transcription levels increased following inoculation with Pst or treatment with flg22 or chitin. TaGW2 knockdown lines showed enhanced resistance to multiple Pst races, while TaGW2 overexpression reduced host defence response, promoted Pst growth and development and increased wheat susceptibility to Pst. Additionally, TaGW2 could mediate the ubiquitination and degradation of both TaSnRK1γ and TaVPS24 via the 26S proteasome pathway. Silencing TaSnRK1γ or TaVPS24 in wheat increased sensitivity to Pst, whereas overexpressing either gene enhanced wheat defence response, indicating that TaSnRK1γ and TaVPS24 act as positive regulators of Pst resistance. This study reveals a previously unrecognized mechanism inhibiting plant immunity to Pst through TaGW2-mediated ubiquitination and degradation of TaSnRK1γ and TaVPS24. This work also provides crucial genetic resources for breeding high-yield, stripe rust-resistant wheat varieties.

Transcriptomic and biochemical analysis of pummelo x finger lime hybrids in response to Huanglongbing (HLB)

BACKGROUND

Huanglongbing (HLB) is a devastating bacterial disease caused by the bacterium Candidatus Liberibacter asiaticus (CaLas) that affects the citrus industry worldwide. This study investigated the response of two pummelo x finger lime hybrid siblings to natural infection with CaLas. The hybrids were identified primarily using leaf morphology and molecular marker assessments and were selected for further studies on the basis of the CaLas titers in leaf petioles.

RESULTS

HLB-infected budwood from the selected hybrids (PFL 2-61 and PFL 1-11), as well as the two parental plants, were propagated by grafting onto Swingle citrumelo rootstocks for further evaluation. Plant samples were collected two years after grafting for analysis. Leaves of PFL2-61 exhibited decreased CaLas titers compared with those of PFL 1-11. Additionally, we recorded increased chlorophyll content, total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity in PFL 2-61 compared to PFL 1-11 and the parents. We subsequently conducted a detailed investigation of these two hybrid siblings using transcriptome analysis. Among the 20,675 differentially expressed genes (DEGs) identified, 1,416 were downregulated in PFL 2-61 compared with PFL 1-11, whereas 326 were upregulated. Transcriptome analysis revealed that many of the DEGs were associated with the cell wall structure, redox homeostasis, and biotic stress responses. Moreover, key genes related to the biosynthesis of secondary metabolites and phytohormones, including PAL1, jasmonate-related genes, and WRKY transcription factors, were upregulated in the tolerant hybrid (PFL 2-61). In contrast, three transcripts associated with the Sieve Element Occlusion N-Terminus (SEO_N) domain were downregulated in the tolerant hybrid (PFL 2-61).

CONCLUSIONS

Our findings provide valuable insights into the molecular mechanisms of tolerance and susceptibility to HLB in finger lime derived hybrids, highlighting the potential of this citrus species towards developing disease-tolerant varieties.

K, Padaria JC, Singh PK, Alam B, Kumar S, Arunachalam A. Validation of stay-green and stem reserve mobilization QTLs: physiological and gene expression approach

Introduction

Abiotic stress significantly reduces the wheat yield by hindering several physiological processes in plant. Stay-green (SG) and stem reserve mobilization (SRM) are the two key physiological traits, which can contribute significantly to grain filling during stress period. Validation of genomic regions linked to SG and SRM is needed for its subsequent use in marker-assisted selection in breeding program.

Methods

Using a physiological and gene expression approach, quantitative trait loci (QTLs) for stay-green (SG) and stem reserve mobilization (SRM) were validated in a pot experiment study using contrasting recombinant inbred lines including its parental lines (HD3086/HI1500) in wheat. The experiment was laid down in a completely randomized design under normal (control, drought) and late sown (heat and combined stress) conditions during the 2022-2023 rabi season. Drought stress was imposed by withholding irrigation at the anthesis stage, whereas heat stress was imposed by 1-month late sowing compared to the normal sowing condition. Combined stress was imposed by 1-month late sowing along with restricted irrigation at the flowering stage. Superior lines (HDHI113 and HDHI87) had both SG and SRM traits, whereas inferior lines (HDHI185 and HDHI80) had contrasting traits, i.e., lower SG and SRM traits. HD3086 and HI1500 had SG and SRM traits respectively. Potential candidate genes were identified based on the flanking markers of the mapped QTLs using the BioMart tool in the Ensembl Plants database to validate the identified QTLs. Real-time gene expression was conducted with SG-linked genes in the flag leaf and SRM-linked genes in the peduncle.

Results and Discussion

In this study, HDHI113 and HDHI87 showed higher expression of SG-related genes in the flag leaf under stress conditions. Furthermore, HDHI113 and HDHI87 maintained higher chlorophyll a content of 7.08 and 6.62 mg/gDW, respectively, and higher net photosynthetic rates (PN) of 17.18 and 16.48 µmol CO2/m2/s, respectively, under the combined stress condition. However, these lines showed higher expression of SRM-linked genes in the peduncle under drought stress, indicating that drought stress aggravates SRM in wheat. HDHI113 and HDHI87 recorded higher 1,000-grain weights and spike weight differences under combined stress, further validating the identified QTLs being linked to SG and SRM traits. Henceforth, the identified QTLs can be transferred to developed wheat varieties through efficient breeding strategies for yield improvement in harsh climate conditions.

Identifications of Genes Involved in ABA and MAPK Signaling Pathways Positively Regulating Cold Tolerance in Rice

Cold stress (CS) significantly impacts rice (Oryza sativa L.) growth during seedling and heading stages. Based on two-year field observations, this study identified two rice lines, L9 (cold stress-sensitive) and LD18 (cold stress-tolerant), showing contrasting CS responses. L9 exhibited a 38% reduction in photosynthetic efficiency, whereas LD18 remained unchanged, correlating with seed rates. Transcriptome analysis identified differentially expressed genes (DEGs) with LD18 showing enriched pathways (carbon fixation, starch/sucrose metabolism, and glutathione metabolism). LD18 displayed dramatically enhanced expression of MAPK-related genes (LOC4342017, LOC9267741, and LOC4342267) and increased ABA signaling genes (LOC4333690, LOC4345611, and LOC4335640) compared with L9 exposed to CS. Results from qPCR confirmed the enhanced expression of the three MAPK-related genes in LD18 with a dramatic reduction in L9 under CS relative to that under CK. We also observed up to 66% reduction in expression levels of the three genes related to the ABA signaling pathway in L9 relative to LD18 under CS. Consistent with the results of photosynthetic efficiency, metabolic analysis suggests pyruvate metabolism, TCA cycle, and carbon metabolism enrichment in LD18 under CS. The study reveals reprogramming of the carbon assimilation metabolic pathways, emphasizing the critical roles of the key DEGs involved in ABA and MAPK signaling pathways in positive regulation of LD18 response to CS, offering the foundation toward cold tolerance breeding through targeted gene editing.

Exploring the Tomato Root Protein Network Exploited by Core Type 3 Effectors from the Ralstonia solanacearum Species Complex

Proteomics has become a powerful approach for the identification and characterization of type III effectors (T3Es). Members of the Ralstonia solanacearum species complex (RSSC) deploy T3Es to manipulate host cells and to promote root infection of, among others, a wide range of solanaceous plants such as tomato, potato, and tobacco. Here, we used TurboID-mediated proximity labeling (PL) in tomato hairy root cultures to explore the proxeomes of the core RSSC T3Es RipU, RipD, and RipB. The RipU proxeome was enriched for multiple protein kinases, suggesting a potential impact on the two branches of the plant immune surveillance system, being the membrane-localized PAMP-triggered immunity (PTI) and the RIN4-dependent effector-triggered immunity (ETI) complexes. In agreement, a transcriptomics analysis in tomato revealed the potential involvement of RipU in modulating reactive oxygen species (ROS) signaling. The proxeome of RipB was putatively enriched for mitochondrial and chloroplast proteins and that of RipD for proteins potentially involved in the endomembrane system. Together, our results demonstrate that TurboID-PL in tomato hairy roots represents a promising tool to study Ralstonia T3E targets and functioning and that it can unravel potential host processes that can be hijacked by the bacterial pathogen.

Mitochondrial AOX1a and an H2O2 feed-forward signalling loop regulate flooding tolerance in rice

Flooding is a widespread natural disaster that causes tremendous yield losses of global food production. Rice is the only cereal capable of growing in aquatic environments. Direct seeding by which seedlings grow underwater is an important cultivation method for reducing rice production cost. Hypoxic germination tolerance and root growth in waterlogged soil are key traits for rice adaptability to flooded environments. Alternative oxidase (AOX) is a non-ATP-producing terminal oxidase in the plant mitochondrial electron transport chain, but its role in hypoxia tolerance had been unclear. We have discovered that AOX1a is necessary and sufficient to promote germination/coleoptile elongation and root development in rice under flooding/hypoxia. Hypoxia enhances endogenous H2O2 accumulation, and H2O2 in turn activates an ensemble of regulatory genes including AOX1a to facilitate the conversion of deleterious reactive oxygen species to H2O2 in rice under hypoxia. We show that AOX1a and H2O2 act interdependently to coordinate three key downstream events, that is, glycolysis/fermentation for minimal ATP production, root aerenchyma development and lateral root emergence under hypoxia. Moreover, we reveal that ectopic AOX1a expression promotes vigorous root and plant growth, and increases grain yield under regular irrigation conditions. Our discoveries provide new insights into a unique sensor-second messenger pair in which AOX1a acts as the sensor perceiving low oxygen tension, while H2O2 accumulation serves as the second messenger triggering downstream root development in rice against hypoxia stress. This work also reveals AOX1a genetic manipulation and H2O2 pretreatment as potential targets for improving flooding tolerance in rice and other crops.

Cytochrome c levels link mitochondrial function to plant growth and stress responses through changes in SnRK1 pathway activity

Energy is required for growth as well as for multiple cellular processes. During evolution, plants developed regulatory mechanisms to adapt energy consumption to metabolic reserves and cellular needs. Reduced growth is often observed under stress, leading to a growth-stress trade-off that governs plant performance under different conditions. In this work, we report that plants with reduced levels of the mitochondrial respiratory chain component cytochrome c (CYTc), required for electron transport coupled to oxidative phosphorylation and ATP production, show impaired growth and increased global expression of stress-responsive genes, similar to those observed after inhibiting the respiratory chain or the mitochondrial ATP synthase. CYTc-deficient plants also show activation of the SnRK1 pathway, which regulates growth, metabolism, and stress responses under carbon starvation conditions, even though their carbohydrate levels are not significantly different from wild-type. Notably, loss-of-function of the gene encoding the SnRK1α1 subunit restores the growth of CYTc-deficient plants, as well as autophagy, free amino acid and TOR pathway activity levels, which are affected in these plants. Moreover, increasing CYTc levels decreases SnRK1 pathway activation, reflected in reduced SnRK1α1 phosphorylation, with no changes in total SnRK1α1 protein levels. Under stress imposed by mannitol, the growth of CYTc-deficient plants is relatively less affected than that of wild-type plants, which is also related to the activation of the SnRK1 pathway. Our results indicate that SnRK1 function is affected by CYTc levels, thus providing a molecular link between mitochondrial function and plant growth under normal and stress conditions.

Exploring sugar allocation and metabolic shifts in cassava plants infected with Cassava common mosaic virus (CsCMV) under long-day photoperiod: diel changes in source and sink leaves

Cassava common mosaic virus (CsCMV) is a potexvirus that impairs chloroplast and metabolism, causing significant yield losses to cassava crops. Crop yield depends on diel rhythms, influencing carbon allocation and growth, and sugar signaling also impacting light-dark rhythms. This study aimed to elucidate the early impact of CsCMV infection on diel carbon allocation, metabolism, and defense mechanisms in both source and sink cassava leaves before storage root bulking. Soluble sugar and starch concentrations were examined over a 24-h cycle (16:8 photoperiod) in CsCMV-infected plants. The expression of an array of genes-carbohydrate metabolism, SnRK1 activity marker, defense, circadian marker-was analyzed at ZT6, ZT16 and ZT24/ZT0. In CsCMV-infected source leaves, at ZT6, sucrose increased whereas glucose, fructose and sucrose rose at night. An increase in Suc:hexose ratio and upregulation of SnRK1 activity marker genes and PR1 transcripts were found in infected leaves, suggesting a combination of altered carbon metabolism and defense response mechanisms against the viral infection. GIGANTEA, a clock-controlled gene, showed a reduced expression in infected leaves at ZT6 and ZT24/ZT0, suggesting a circadian phase shift compared with uninfected control plants. Additionally, starch mobilization transcripts were downregulated at ZT24/ZT0, though starch content remained unchanged during the 24-h cycle. In sink leaves, a transient peak of maltose (ZT6) was observed. Our findings suggest that CsCMV disrupts the plant's natural rhythms of sugar metabolism and allocation. Spikes in sucrose levels may serve as infection signals in the internal daily clock of the plant, influencing plant responses during the cassava-CsCMV interaction.

A mechanistic integration of hypoxia signaling with energy, redox, and hormonal cues

Oxygen deficiency (hypoxia) occurs naturally in many developing plant tissues but can become a major threat during acute flooding stress. Consequently, plants as aerobic organisms must rapidly acclimate to hypoxia and the associated energy crisis to ensure cellular and ultimately organismal survival. In plants, oxygen sensing is tightly linked with oxygen-controlled protein stability of group VII ETHYLENE-RESPONSE FACTORs (ERFVII), which, when stabilized under hypoxia, act as key transcriptional regulators of hypoxia-responsive genes (HRGs). Multiple signaling pathways feed into hypoxia signaling to fine-tune cellular decision-making under stress. First, ATP shortage upon hypoxia directly affects the energy status and adjusts anaerobic metabolism. Secondly, altered redox homeostasis leads to reactive oxygen and nitrogen species (ROS and RNS) accumulation, evoking signaling and oxidative stress acclimation. Finally, the phytohormone ethylene promotes hypoxia signaling to improve acute stress acclimation, while hypoxia signaling in turn can alter ethylene, auxin, abscisic acid, salicylic acid, and jasmonate signaling to guide development and stress responses. In this Update, we summarize the current knowledge on how energy, redox, and hormone signaling pathways are induced under hypoxia and subsequently integrated at the molecular level to ensure stress-tailored cellular responses. We show that some HRGs are responsive to changes in redox, energy, and ethylene independently of the oxygen status, and we propose an updated HRG list that is more representative for hypoxia marker gene expression. We discuss the synergistic effects of hypoxia, energy, redox, and hormone signaling and their phenotypic consequences in the context of both environmental and developmental hypoxia.

Metabolic strategies in hypoxic plants

Complex multicellular organisms have evolved in an oxygen-enriched atmosphere. Oxygen is therefore essential for all aerobic organisms, including plants, for energy production through cellular respiration. However, plants can experience hypoxia following extreme flooding events and also under aerated conditions in proliferative organs or tissues characterized by high oxygen consumption. When oxygen availability is compromised, plants adopt different strategies to cope with hypoxia and limited aeration. A common feature among different plant species is the activation of an anaerobic fermentative metabolism to provide ATP to maintain cellular homeostasis under hypoxia. Fermentation also requires many sugar substrates, which is not always feasible, and alternative metabolic strategies are thus needed. Recent findings have also shown that the hypoxic metabolism is also active in specific organs or tissues of the plant under aerated conditions. Here, we describe the regulatory mechanisms that control the metabolic strategies of plants and how they enable them to thrive despite challenging conditions. A comprehensive mechanistic understanding of the genetic and physiological components underlying hypoxic metabolism should help to provide opportunities to improve plant resilience under the current climate change scenario.

Carbon and nitrogen signaling regulate FLOWERING LOCUS C and impact flowering time in Arabidopsis

The timing of flowering in plants is modulated by both carbon (C) and nitrogen (N) signaling pathways. In a previous study, we established a pivotal role of the sucrose-signaling trehalose 6-phosphate pathway in regulating flowering under N-limited short-day conditions. In this work, we show that both wild-type Arabidopsis (Arabidopsis thaliana) plants grown under N-limited conditions and knock-down plants of TREHALOSE PHOSPHATE SYNTHASE 1 induce FLOWERING LOCUS C (FLC) expression, a well-known floral repressor associated with vernalization. When exposed to an extended period of cold, a flc mutant fails to respond to N availability and flowers at the same time under N-limited and full-nutrition conditions. Our data suggest that SUCROSE NON-FERMENTING 1 RELATED KINASE 1-dependent trehalose 6-phosphate-mediated C signaling and a mechanism downstream of N signaling (likely involving NIN-LIKE PROTEIN 7) impact the expression of FLC. Collectively, our data underscore the existence of a multi-factor regulatory system in which the C and N signaling pathways jointly govern the regulation of flowering in plants.

Pesticide-induced metabolic disruptions in crops: A global perspective at the molecular level

Pesticide pollution has emerged as a critical global environmental issue of pervasive concern. Although the application of pesticides has provided substantial benefits in controlling weeds, pests, and crop diseases, their indiscriminate use poses considerable challenges to soil health and food safety. Pesticides can be absorbed by crops through either foliar or root uptake, resulting in deleterious effects such as extensive tissue damage, growth inhibition, and reduced crop quality. Beside these visible effects, pesticides can alter gene expression and disrupt cellular signaling transduction, thereby interfering with essential metabolic processes even inducing toxic stress. Moreover, pesticides can interact intricately with biomolecules (e.g. proteins, nucleic acid) in crops, causing significant alterations in protein structure and physiological function. This review focuses on pesticide residues and their associated toxicity, emphasizing their pervasive influence on vital physiological and metabolic pathways, including carbohydrate metabolism, amino acid metabolism, and fatty acid metabolism. Particular attention is given to elucidating the molecular mechanisms underlying these disturbances, specifically regarding transcriptional regulation, cell signaling pathways, and biomolecular interactions. This review provides a comprehensive understanding of multifaceted effects of pesticides and to underscore the necessity for sustainable agricultural practices to safeguard crop yield and quality.

The role of trehalose metabolism in plant stress tolerance

BACKGROUND

Trehalose is a nonreducing disaccharide containing two glucose molecules linked through an α,α-1,1-glycosidic bond. This unique chemical structure causes trehalose levels to fluctuate significantly in plants under stress, where it functions as an osmoprotectant, enhancing plant resistance to stress. Previous studies have confirmed that the trehalose synthesis pathway is widely conserved across most plants. However, the protective role of trehalose is limited only to organelles or tissues where the concentration is sufficiently high.

AIM OF REVIEW

In this review, we summarize previous reports on improving plant stress tolerance (drought, cold, heat, salt, pathogen, etc.) by applying trehalose-6-phosphate (T6P) or trehalose and manipulating the expression of trehalose metabolism-related genes. The molecular mechanisms underlying T6P, trehalose, and their related genes that regulate plant stress resistance are reviewed. More progressive studies on the spatiotemporal control of trehalose metabolism will provide a novel tool that allows for the simultaneous enhancement of crop yield and stress tolerance.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We introduce the history of trehalose and discuss the possibility of trehalose and its metabolity-related genes binding to T6P to participate in stress response through unknown signaling pathways. In addition, the effects of trehalose metabolism regulation on plant growth and stress resistance were reviewed, and the molecular mechanism was fully discussed. In particular, we came up with new insights that the molecular mechanism of trehalose metabolism to enhance plant stress resistance in the future and we propose the need to use biotechnology methods to cultivate crops with stress resistance and high yield potential.

Senescence-Associated Sugar Transporter1 affects developmental master regulators and controls senescence in Arabidopsis

Sugar transport across membranes is critical for plant development and yield. However, an analysis of the role of intracellular sugar transporters in senescence is lacking. Here, we characterized the role of Senescence-Associated Sugar Transporter1 (SAST1) during senescence in Arabidopsis (Arabidopsis thaliana). SAST1 expression was induced in leaves during senescence and after the application of abscisic acid (ABA). SAST1 is a vacuolar protein that pumps glucose out of the cytosol. sast1 mutants exhibited a stay-green phenotype during developmental senescence, after the darkening of single leaves, and after ABA feeding. To explain the stay-green phenotype of sast1 mutants, we analyzed the activity of the glucose-induced master regulator TOR (target of rapamycin), which is responsible for maintaining a high anabolic state. TOR activity was higher in sast1 mutants during senescence compared to wild types, whereas the activity of its antagonist, SNF1-related protein kinase 1 (SnRK1), was reduced in sast1 mutants under senescent conditions. This deregulation of TOR and SnRK1 activities correlated with high cytosolic glucose levels under senescent conditions in sast1 mutants. Although sast1 mutants displayed a functional stay-green phenotype, their seed yield was reduced. These analyses place the activity of SAST1 in the last phase of a leaf's existence in the molecular program required to complete its life cycle.

Effects of high temperature on grain quality and enzyme activity in heat-sensitive versus heat-tolerant rice cultivars

BACKGROUND

High-temperature (HT) stress significantly affects the quality of rice (Oryza sativa L.), although the underlying the mechanism remains unknown. Therefore, in the present study, we assessed protein components, amino acids, mineral element levels, starch biosynthesis enzyme activity and gene expression of two heat-sensitive and two heat-tolerant genotypes under HT treatment during early (from 1 to 10 days, T1) and mid-filling (from 11 to 20 days, T2) after anthesis.

RESULTS

Except for one cultivar, most rice varieties exhibited increased levels of amylose, chalky degree and protein content, along with elevated cracked grains and pasting temperatures and, consequently, suppressed amino acid levels under HT stress. HT treatment also increased protein components, macro- (Mg, K, P and S) and microelements (Cu, Zn, and Mo) in the rice flour. Both HT treatments reduced the activity of ADP-glucose pyrophosphate, ground-bound starch synthase, as well as the relative ratio of amylose to total starch, at the same time increasing starch branch enzyme activity. The expression levels of OsAGPL2, OsSSS1 and OsSBE1 in all varieties exhibited the same trends as enzyme activity under HT treatment.

CONCLUSION

High temperatures negatively affected rice quality during grain filling, which is related to heat tolerance and grain shape. Altered enzymatic activity is crucial to compensate for the lowered enzyme quality under heat stress. © 2024 Society of Chemical Industry.

Perception and processing of stress signals by plant mitochondria

In the course of their life, plants continuously experience a wide range of unfavourable environmental conditions in the form of biotic and abiotic stress factors. The perception of stress via various organelles and rapid, tailored cellular responses are essential for the establishment of plant stress resilience. Mitochondria as the biosynthetic sites of energy equivalents in the form of ATP-provided in order to enable a multitude of biological processes in the cell-are often directly impacted by external stress factors. At the same time, mitochondrial function may fluctuate to a tolerable extent without the need to activate downstream retrograde signalling cascades for stress adaptation. In this Focus Review, we summarise the current state of knowledge on the perception and processing of stress signals by mitochondria and show which layers of retrograde signalling, that is, those involving transcription factors, metabolites, but also enzymes with moonlighting functions, enable communication with the nucleus. Also, light is shed on signal integration between mitochondria and chloroplasts as part of retrograde signalling. With this Focus Review, we aim to show ways in which organelle-specific communication can be further researched and the collected data used in the long-term to strengthen plant resilience in the context of climate change.

Genome-Wide Identification of FCS-Like Zinc Finger (FLZ) Family Genes in Three Brassica Plant Species and Functional Characterization of BolFLZs in Chinese Kale Under Abiotic Stresses

FCS-like zinc finger (FLZ) proteins are plant-specific regulatory proteins, which contain a highly conserved FLZ domain, and they play critical roles in plant growth and stress responses. Although the FLZ family has been systematically characterized in certain plants, it remains underexplored in Brassica species, which are vital sources of vegetables, edible oils, and condiments for human consumption and are highly sensitive to various abiotic stresses. Following the whole-genome triplication events (WGT) in Brassica, elucidating how the FLZ genes have expanded, differentiated, and responded to abiotic stresses is valuable for uncovering the genetic basis and functionality of these genes. In this study, we identified a total of 113 FLZ genes from three diploid Brassica species and classified them into four groups on the basis of their amino acid sequences. Additionally, we identified 109 collinear gene pairs across these Brassica species, which are dispersed among different chromosomes, suggesting that whole-genome duplication (WGD) has significantly contributed to the expansion of the FLZ family. Subcellular localization revealed that six representative BolFLZ proteins are located in the nucleus and cytoplasm. Yeast two-hybrid assays revealed that 13 selected BolFLZs interact with BolSnRK1α1 and BolSnRK1α2, confirming the conservation of the SnRK1α-FLZ module in Brassica species. Expression profile analysis revealed differential expression patterns of BolFLZ across various tissues. Notably, the expression levels of seven BolFLZ genes out of the fifteen genes analyzed changed significantly following treatment with various abiotic stressors, indicating that the BolFLZ genes play distinct physiological roles and respond uniquely to abiotic stresses in Brassica species. Together, our results provide a comprehensive overview of the FLZ gene family in Brassica species and insights into their potential applications for enhancing stress tolerance and growth in Chinese kale.

14-3-3 proteins inhibit autophagy by regulating SINAT-mediated proteolysis of ATG6 in Arabidopsis

BACKGROUND

Autophagy is a conserved cellular process crucial for recycling cytoplasmic components and maintaining cellular homeostasis in eukaryotes. During autophagy, the formation of a protein complex involving AUTOPHAGY-RELATED PROTEIN 6 (ATG6) and phosphatidylinositol 3-kinase is pivotal for recruiting proteins involved in phagophore expansion. However, the intricate molecular mechanism regulating this protein complex in plants remains elusive.

RESULTS

Here, we aimed to unravel the molecular regulation of autophagy dynamics in Arabidopsis thaliana by investigating the involvement of the scaffold proteins 14-3-3λ and 14-3-3κ in regulating the proteolysis of ATG6. Phenotypic analyses revealed that 14-3-3λ and 14-3-3κ overexpression lines exhibited increased sensitivity to nutrient starvation, premature leaf senescence, and a decrease in starvation-induced autophagic vesicles, resembling the phenotypes of autophagy-defective mutants, suggesting the potential roles of 14-3-3 proteins in regulating autophagy in plants. Furthermore, our investigation unveiled the involvement of 14-3-3λ and 14-3-3κ in the RING finger E3 ligase SINAT1-mediated ubiquitination and destabilization of ATG6 in vivo. We also observed repressed turnover of ATG6 and translocation of GFP-ATG6 to mCherry-ATG8a-labelled punctate structures in the autophagy-defective mutant, which suggesting that ATG6 is probably a target of autophagy. Additionally, 14-3-3λ and 14-3-3κ interacted with Tumor necrosis factor Receptor Associated Factor 1a (TRAF1a) to promote the stability of TRAF1a in vivo under nutrient-rich conditions, suggesting a feedback regulation of autophagy. These findings demonstrate that 14-3-3λ and 14-3-3κ serve as scaffold proteins to regulate autophagy by facilitating the SINAT1-mediated proteolysis of ATG6, involving both direct and indirect mechanisms, in plants.

CONCLUSIONS

14-3-3 proteins regulate autophagy by directly or indirectly binding to ATG6 and SINAT1 to promote ubiquitination and degradation of ATG6. 14-3-3 proteins are involved in modulating autophagy dynamics by facilitating SINAT1-mediated ubiquitination and degradation of ATG6.

Trade-Off Regulation in Plant Growth and Stress Responses Through the Role of Heterotrimeric G Protein Signaling

Unlike animals, plants are sessile organisms that cannot migrate to more favorable conditions and must constantly adapt to a variety of biotic and abiotic stresses. Therefore, plants exhibit developmental plasticity to cope, which is probably based on the underlying trade-off mechanism that allocates energy expenditure between growth and stress responses to achieve appropriate growth and development under different environmental conditions. Plant heterotrimeric G protein signaling plays a crucial role in the trade-off involved in the regulation of normal growth and stress adaptation. This review examines the composition and signaling processes of heterotrimeric G proteins in plants, detailing how they balance growth and adaptive responses in plant immunity and thermomorphogenesis through recent advances in the field. Understanding the trade-offs associated with plant G protein signaling will have significant implications for agricultural innovation, particularly in the development of crops with improved resilience and minimal growth penalties under environmental stress.

A maize WAK-SnRK1α2-WRKY module regulates nutrient availability to defend against head smut disease

Obligate biotrophs depend on living hosts for nutrient acquisition to complete their life cycle, yet the mechanisms by which hosts restrict nutrient availability to pathogens remain largely unknown. The fungal pathogen Sporisorium reilianum infects maize seedlings and causes head smut disease in inflorescences at maturity, while a cell wall-associated kinase, ZmWAK, provides quantitative resistance against it. In this study, we demonstrate that S. reilianum can rapidly activate ZmWAK kinase activity, which is sustained by the 407th threonine residue in the juxtamembrane domain, enabling it to interact with and phosphorylate ZmSnRK1α2, a conserved sucrose non-fermenting-related kinase α subunit. The activated ZmSnRK1α2 translocates from the cytoplasm to the nucleus, where it phosphorylates and destabilizes the transcription factor ZmWRKY53. The reduced ZmWRKY53 abundance leads to the downregulation of genes involved in transmembrane transport and carbohydrate metabolism, resulting in nutrient starvation for S. reilianum in the apoplast. Collectively, our study uncovers a WAK-SnRK1α2-WRKY53 signaling module in maize that conveys phosphorylation cascades from the plasma membrane to the nucleus to confer plant resistance against head smut in maize, offering new insights and potential targets for crop disease management.

PRL1 interacts with and stabilizes RPA2A to regulate carbon deprivation-induced senescence in Arabidopsis

Leaf senescence is a developmental program regulated by both endogenous and environmental cues. Abiotic stresses such as nutrient deprivation can induce premature leaf senescence, which profoundly impacts plant growth and crop yield. However, the molecular mechanisms underlying stress-induced senescence are not fully understood. In this work, employing a carbon deprivation (C-deprivation)-induced senescence assay in Arabidopsis seedlings, we identified PLEIOTROPIC REGULATORY LOCUS 1 (PRL1), a component of the NineTeen Complex, as a negative regulator of C-deprivation-induced senescence. Furthermore, we demonstrated that PRL1 directly interacts with the RPA2A subunit of the single-stranded DNA-binding Replication Protein A (RPA) complex. Consistently, the loss of RPA2A leads to premature senescence, while increased expression of RPA2A inhibits senescence. Moreover, overexpression of RPA2A reverses the accelerated senescence in prl1 mutants, and the interaction with PRL1 stabilizes RPA2A under C-deprivation. In summary, our findings reveal the involvement of the PRL1-RPA2A functional module in C-deprivation-induced plant senescence.

Role of auxin and gibberellin under low light in enhancing saffron corm starch degradation during sprouting

The mechanisms by which low light accelerates starch macromolecules degradation by auxin and gibberellin (GA) in geophytes during sprouting remain largely unknown. This study investigated these mechanisms in saffron, grown under low light (50 μmol m-2 s-1) and optimal light (200 μmol m-2 s-1) during the sprouting phase. Low light reduced starch concentration in corms by 34.0 % and increased significantly sucrose levels in corms, leaves, and leaf sheaths by 19.2 %, 9.8 %, and 134.5 %, respectively. This was associated with a 33.3 % increase in GA3 level and enhanced auxin signaling. Leaves synthesized IAA under low light, which was transported to the corms to promote GA synthesis, facilitating starch degradation through a 228.7 % increase in amylase activity. Exogenous applications of GA and IAA, as well as the use of their synthesis or transport inhibitors, confirmed the synergistic role of these phytohormones in starch metabolism. The unigenes associated with GA biosynthesis and auxin signaling were upregulated under low light, highlighting the IAA-GA module role in starch degradation. Moreover, increased respiration rate and invertase activity, crucial for ATP biosynthesis and the tricarboxylic acid cycle, were consistent with the upregulation of related unigenes, suggesting that auxin signaling accelerates starch degradation by promoting energy metabolism. Upregulated of auxin signaling (CsSAUR32) and starch metabolism (CsSnRK1) genes under low light suggests that auxin directly regulate starch degradation in saffron corms. This study elucidates that low light modulates auxin and GA interactions to accelerate starch degradation in saffron corms during sprouting, offering insights for optimizing agricultural practices under suboptimal light conditions.

Ferroptosis, oxidative stress and hearing loss: Mechanistic insights and therapeutic opportunities

Hearing loss, a prevalent sensory impairment, poses significant challenges worldwide. Recent research has shed light on the intricate interplay between ferroptosis, a newly recognized form of regulated cell death characterized by iron-dependent lipid peroxidation, and oxidative stress in the pathogenesis of hearing loss. In this review, we delve into the mechanisms underlying ferroptosis and oxidative stress in various forms of hearing loss, including age-related hearing loss (ARHL), noise-induced hearing loss (NIHL) ototoxic drug-induced hearing loss and genetic hearing loss. We discuss the pivotal role of molecules such as FSP1, ACSL4, LKB1-AMPK, and Nrf2 in modulating these pathways in hearing loss. Furthermore, we explore emerging therapeutic strategies targeting the antioxidant system and ferroptosis, including iron chelators, lipid peroxide inhibitors, and antioxidants, highlighting their potential in mitigating hearing loss progression. By elucidating the molecular mechanisms underlying ferroptosis and oxidative stress, this review offers insights into novel therapeutic avenues for the treatment of hearing loss and underscores the importance of targeting these pathways to preserve auditory function.

Bioinformatic insights into sugar signaling pathways in sugarcane growth

The SnRK1, hexokinase, and TORC1 (TOR, LST8, RAPTOR) are three pivotal kinases at the core of sugar level sensing, significantly impacting plant metabolism and development. We retrieved and analyzed protein sequences of these three kinase pathways from seven sugarcane transcriptome and genome datasets, identifying protein domains, phylogenetic relationships, sequence ancestry, and in silico expression levels. Additionally, we predicted HXK subcellular localization and assessed its enzymatic activity in sugarcane leaves and culms along development in the field. We retrieved 11 TOR, 23 RAPTOR, 55 LST8, 95 SnRK1α, 98 HXK, and 14 HXK-like putative full-length sequences containing all the conserved domains. Most of these transcripts seem to share a common origin with the three ancestral species of sugarcane: Saccharum officinarum, Saccharum spontaneum, and Saccharum barberi. We accessed the expression profile of sequences from one sugarcane transcriptome. We found the highest enzymatic activity of HXK in culms in the first month, which, at this stage, provides carbon (sucrose) and nitrogen (amino acids) for initial plant development. Our approach places novel sugar sensing sequences that work as a guideline for further research into the underlying signaling mechanisms and biotechnology applications in sugarcane.

Molecular advances in bud dormancy in trees

Seasonal bud dormancy in perennial woody plants is a crucial and intricate process that is vital for the survival and development of plants. Over the past few decades, significant advancements have been made in understanding many features of bud dormancy, particularly in model species, where certain molecular mechanisms underlying this process have been elucidated. We provide an overview of recent molecular progress in understanding bud dormancy in trees, with a specific emphasis on the integration of common signaling and molecular mechanisms identified across different tree species. Additionally, we address some challenges that have emerged from our current understanding of bud dormancy and offer insights for future studies.

Similar chilling response of dormant buds in potato tuber and woody perennials

Bud dormancy is a survival strategy that plants have developed in their native habitats. It helps them endure harsh seasonal changes by temporarily halting growth and activity until conditions become more favorable. Research has primarily focused on bud dormancy in tree species and the ability to halt growth in vegetative tissues, particularly in meristems. Various plant species, such as potato, have developed specialized storage organs, enabling them to become dormant during their yearly growth cycle. Deciduous trees and potato tubers exhibit a similar type of bud endodormancy, where the bud meristem will not initiate growth, even under favorable environmental conditions. Chilling accumulation activates C-repeat/dehydration responsive element binding (DREB) factors (CBFs) transcription factors that modify the expression of dormancy-associated genes. Chilling conditions shorten the duration of endodormancy by influencing plant hormones and sugar metabolism, which affect the timing and rate of bud growth. Sugar metabolism and signaling pathways can interact with abscisic acid, affecting the symplastic connection of dormant buds. This review explores how chilling affects endodormancy duration and explores the similarity of the chilling response of dormant buds in potato tubers and woody perennials.

Emerging into the world: regulation and control of dormancy and sprouting in geophytes

Geophytic plants synchronize growth and quiescence with the external environment to survive and thrive under changing seasons. Together with seasonal growth adaptation, dormancy and sprouting are critical factors determining crop yield and market supply, as various geophytes also serve as major food, floriculture, and ornamental crops. Dormancy in such crops determines crop availability in the market, as most of them are consumed during the dormant stage. On the other hand, uniform/maximal sprouting is crucial for maximum yield. Thus, dormancy and sprouting regulation have great economic importance. Dormancy-sprouting cycles in geophytes are regulated by genetic, exogenous (environmental), and endogenous (genetic, metabolic, hormonal, etc.) factors. Comparatively, the temperature is more dominant in regulating dormancy and sprouting in geophytes, unlike above-ground tissues, where both photoperiod and temperature control are involved. Despite huge economic importance, studies concerning the regulation of dormancy and sprouting are scarce in the majority of geophytes. To date, only a few molecular factors involved in the process have been suggested. Recently, omics studies on molecular and metabolic factors involved in dormancy and growth regulation of underground vegetative tissues have provided more insight into the mechanism. Here, we discuss current knowledge of the environmental and molecular regulation and control of dormancy and sprouting in geophytes, and discuss challenges/questions that need to be addressed in the future for crop improvement.

A Nitrogen-specific Interactome Analysis Sheds Light on the Role of the SnRK1 and TOR Kinases in Plant Nitrogen Signaling

Nitrogen (N) is of utmost importance for plant growth and development. Multiple studies have shown that N signaling is tightly coupled with carbon (C) levels, but the interplay between C/N metabolism and growth remains largely an enigma. Nonetheless, the protein kinases Sucrose Non-fermenting 1 (SNF1)-Related Kinase 1 (SnRK1) and Target Of Rapamycin (TOR), two ancient central metabolic regulators, are emerging as key integrators that link C/N status with growth. Despite their pivotal importance, the exact mechanisms behind the sensing of N status and its integration with C availability to drive metabolic decisions are largely unknown. Especially for SnRK1, it is not clear how this kinase responds to altered N levels. Therefore, we first monitored N-dependent SnRK1 kinase activity with an in vivo Separation of Phase-based Activity Reporter of Kinase (SPARK) sensor, revealing a contrasting N-dependency in Arabidopsis thaliana (Arabidopsis) shoot and root tissues. Next, using affinity purification (AP) and proximity labeling (PL) coupled to mass spectrometry (MS) experiments, we constructed a comprehensive SnRK1 and TOR interactome in Arabidopsis cell cultures during N-starved and N-repleted growth conditions. To broaden our understanding of the N-specificity of the TOR/SnRK1 signaling events, the resulting network was compared to corresponding C-related networks, identifying a large number of novel, N-specific interactors. Moreover, through integration of N-dependent transcriptome and phosphoproteome data, we were able to pinpoint additional N-dependent network components, highlighting for instance SnRK1 regulatory proteins that might function at the crosstalk of C/N signaling. Finally, confirmation of known and identification of novel SnRK1 interactors, such as Inositol-Requiring 1 (IRE1A) and the RAB GTPase RAB18, indicate that SnRK1, present at the ER, is involved in N signaling and autophagy induction.

SnRK1/TOR/T6P: three musketeers guarding energy for root growth

Sugars derived from photosynthesis, specifically sucrose, are the primary source of plant energy. Sucrose is produced in leaves and transported to the roots through the phloem, serving as a vital energy source. Environmental conditions can result in higher or lower photosynthesis, promoting anabolism or catabolism, respectively, thereby influencing the sucrose budget available for roots. Plants can adjust their root system to optimize the search for soil resources and to ensure the plant's adaptability to diverse environmental conditions. Recently, emerging research indicates that SNF1-RELATED PROTEIN KINASE 1 (SnRK1), trehalose 6-phosphate (T6P), and TARGET OF RAPAMYCIN (TOR) collectively serve as fundamental regulators of root development, together forming a signaling module to interpret the nutritional status of the plant and translate this to growth adjustments in the below ground parts.

HXK, SnRK1, and TOR signaling in plants: Unraveling mechanisms of stress response and secondary metabolism

As sessile photoautotrophs, plants constantly encounter diverse environmental stresses. Recent research has focused on elucidating sugar and energy signaling mediated by hexokinase (HXK), sucrose non-fermenting 1-related protein kinase 1 (SnRK1), and the target of rapamycin (TOR) and assessing its intricate interplay with hormones and secondary metabolism. HXK serves as a pivotal regulator of glucose sensing and metabolism. It affects plant growth and development in response to nutrient availability. SnRK1 acts as a vital energy sensor that regulates metabolic adjustments during stress to bolster plant resilience. Moreover, TOR integrates nutrient signals to finely modulate growth and development, balancing cellular metabolism and resource allocation. Understanding the functions of HXK, SnRK1, and TOR can provide profound insights into plant adaptation mechanisms and open promising avenues for leveraging biotechnological strategies to enhance the stress tolerance and nutritional value of crops. This narrative review focuses on recent advancements in the molecular mechanisms of HXK, SnRK1, and TOR and explores their potential applications in agricultural biotechnology.

Identification and characterisation of 'No apical meristem; Arabidopsis transcription activation factor; Cup-shape cotyledon' (NAC) family transcription factors involved in sugar accumulation and abscisic acid signalling in grape (Vitis vinifera)

The 'No apical meristem; Arabidopsis transcription activation factor; Cup-shape cotyledon' (NAC) transcription factors are pivotal in plant development and stress response. Sucrose-non-fermenting-related protein kinase 1.2 (SnRK1) is a key enzyme in glucose metabolism and ABA signalling. In this study, we used grape (Vitis vinifera ) calli to explore NAC's roles in sugar and ABA pathways and its relationship with VvSnRK1.2 . We identified 19 VvNACs highly expressed at 90days after blooming, coinciding with grape maturity and high sugar accumulation, and 11 VvNACs randomly selected from 19 were demonstrated in response to sugar and ABA treatments. VvNAC26 showed significant response to sugar and ABA treatments, and its protein, as a nucleus protein, had transcriptional activation in yeast. We obtained the overexpression (OE-VvNAC26 ) and RNA-inhibition (RNAi-VvNAC26 ) of VvNAC26 in transgenic calli by Agrobacterium tumefaciens -mediated transformation. We found that VvNAC26 negatively influenced fructose content. Under sugar and ABA treatments, VvNAC26 negatively influenced the expression of most sugar-related genes, while positively influencing the expression of most ABA pathway-related genes. Dual-luciferase reporter experiments demonstrated that VvNAC26 significantly upregulates VvSnRK1.2 promoter expression in tobacco (Nicotiana benthamiana ) leaves, although this process in grape calli requires ABA. The levels of sugar content, sugar-related genes, and ABA-related genes fluctuated significantly in OE-VvNAC26 +RNAi-VvSnRK1.2 and OE-VvSnRK1.2 +RNAi-VvNAC26 transgenic calli. These findings indicated that VvNAC26 regulates sugar metabolism and ABA pathway, displaying synergistic interactions with VvSnRK1.2 .

Transcriptomic and Metabolomic Profiling of Root Tissue in Drought-Tolerant and Drought-Susceptible Wheat Genotypes in Response to Water Stress

Wheat is the most widely grown crop in the world; its production is severely disrupted by increasing water deficit. Plant roots play a crucial role in the uptake of water and perception and transduction of water deficit signals. In the past decade, the mechanisms of drought tolerance have been frequently reported; however, the transcriptome and metabolome regulatory network of root responses to water stress has not been fully understood in wheat. In this study, the global transcriptomic and metabolomics profiles were employed to investigate the mechanisms of roots responding to water stresses using the drought-tolerant (DT) and drought-susceptible (DS) wheat genotypes. The results showed that compared with the control group, wheat roots exposed to polyethylene glycol (PEG) had 25941 differentially expressed genes (DEGs) and more upregulated genes were found in DT (8610) than DS (7141). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs of the drought-tolerant genotype were preferably enriched in the flavonoid biosynthetic process, anthocyanin biosynthesis and suberin biosynthesis. The integrated analysis of the transcriptome and metabolome showed that in DT, the KEGG pathways, including flavonoid biosynthesis and arginine and proline metabolism, were shared by differentially accumulated metabolites (DAMs) and DEGs at 6 h after treatment (HAT) and pathways including alanine, aspartate, glutamate metabolism and carbon metabolism were shared at 48 HAT, while in DS, the KEGG pathways shared by DAMs and DEGs only included arginine and proline metabolism at 6 HAT and the biosynthesis of amino acids at 48 HAT. Our results suggest that the drought-tolerant genotype may relieve the drought stress by producing more ROS scavengers, osmoprotectants, energy and larger roots. Interestingly, hormone signaling plays an important role in promoting the development of larger roots and a higher capability to absorb and transport water in drought-tolerant genotypes.

Virus-Induced galactinol-sucrose galactosyltransferase 2 Silencing Delays Tomato Fruit Ripening

Tomato fruit ripening is an elaborate genetic trait correlating with significant changes at physiological and biochemical levels. Sugar metabolism plays an important role in this highly orchestrated process and ultimately determines the quality and nutritional value of fruit. However, the mode of molecular regulation is not well understood. Galactinoal-sucrose galactosyltransferase (GSGT), a key enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs), can transfer the galactose unit from 1-α-D-galactosyl-myo-inositol to sucrose and yield raffinose, or catalyze the reverse reaction. In the present study, the expression of SlGSGT2 was decreased by Potato Virus X (PVX)-mediated gene silencing, which led to an unripe phenotype in tomato fruit. The physiological and biochemical changes induced by SlGSGT2 silencing suggested that the process of fruit ripening was delayed as well. SlGSGT2 silencing also led to significant changes in gene expression levels associated with ethylene production, pigment accumulation, and ripening-associated transcription factors (TFs). In addition, the interaction between SlGSGT2 and SlSPL-CNR indicated a possible regulatory mechanism via ripening-related TFs. These findings would contribute to illustrating the biological functions of GSGT2 in tomato fruit ripening and quality forming.

Sugar signaling modulates SHOOT MERISTEMLESS expression and meristem function in Arabidopsis

In plants, development of all above-ground tissues relies on the shoot apical meristem (SAM) which balances cell proliferation and differentiation to allow life-long growth. To maximize fitness and survival, meristem activity is adjusted to the prevailing conditions through a poorly understood integration of developmental signals with environmental and nutritional information. Here, we show that sugar signals influence SAM function by altering the protein levels of SHOOT MERISTEMLESS (STM), a key regulator of meristem maintenance. STM is less abundant in inflorescence meristems with lower sugar content, resulting from plants being grown or treated under limiting light conditions. Additionally, sucrose but not light is sufficient to sustain STM accumulation in excised inflorescences. Plants overexpressing the α1-subunit of SUCROSE-NON-FERMENTING1-RELATED KINASE 1 (SnRK1) accumulate less STM protein under optimal light conditions, despite higher sugar accumulation in the meristem. Furthermore, SnRK1α1 interacts physically with STM and inhibits its activity in reporter assays, suggesting that SnRK1 represses STM protein function. Contrasting the absence of growth defects in SnRK1α1 overexpressors, silencing SnRK1α in the SAM leads to meristem dysfunction and severe developmental phenotypes. This is accompanied by reduced STM transcript levels, suggesting indirect effects on STM. Altogether, we demonstrate that sugars promote STM accumulation and that the SnRK1 sugar sensor plays a dual role in the SAM, limiting STM function under unfavorable conditions but being required for overall meristem organization and integrity under favorable conditions. This highlights the importance of sugars and SnRK1 signaling for the proper coordination of meristem activities.